Hello and welcome to my blog! My name is Caroline and I am a PhD student at the University of Sheffield. My research project focuses on Striga - a genus of parasitic plants that devastates harvests by infecting food crops. I am exploring the defence reactions that can make host plants more resistant against Striga. Due to my ongoing battles with anorexia, I haven't made as much progress as I would have liked but I am determined to finish the course.

This blog charts the ups and downs of life in the lab, plus my dreams to become a science communicator and forays into public engagement and science policy....all while trying to keep my mental and physical health intact. Along the way, I'll also be sharing new plant science stories, and profiles of some of the researchers who inspire me on this journey. So whether you have a fascination for plants, are curious about what science research involves, or just wonder what exactly I do all day, read on - I hope you find it entertaining!

Saturday 26 October 2013

Getting my fingers dirty...

You can't be a plant scientist without plants of course. After weeks of feeling like a "paper student", engrossed in admin and a literature review, I am finally starting my proper induction to the lab.

It seems ironic that, although these parasites run rampant in the countries they affect, it can be surprisingly tricky to grow them in this country, even under the controlled conditions the lab and growth room allow. Nevertheless, the Scholes lab has got this down to a fine art, with precise timings, meticulous watering regimes, accurate chemical concentrations of germination stimulants...etc. I have grown Arabidopsis (thale cress; the model organisms of the plant science world, with the most heavily annotated genome of any plant), Wheat and Sorghum before but working on multiple systems at once is a new challenge. First there are the crops themselves. I have successfully managed to germinate rice seedlings and am growing these up to infect with Striga next week. The problem is, these plants can take up a fair bit of space...hence the rhizotron system. Rather than growing the seedlings in pots, the roots are trained into large, flat square petri dishes packed with vermiculite (which looks like an inedible form of muesli); these are then covered in foil to simulate below ground conditions. The petri dishes are packed together in trays, the young leaves poking out of a hole at the top, each with a "dripper" for irrigation. The Striga seeds, meanwhile, are prepared in an incubator in the lab; like Orobanche, these require a few weeks of "pre-conditioning" - being coddled in warm, moist conditions. This makes them responsive to germination stimulant. Because parasite seeds are tiny (no, really, miniscule, like dust!), they have little reserves so have developed a clever strategy where they only germinate in the the presence of a suitable host that they can rapidly infect. To do this, they have evolved the ability to recognise chemical compounds naturally secreted by hosts in the root exudates, called "germination stimulants". In the case of Striga, these compounds are classed as "Strigolactones", which also have a role as a plant hormone in the host, to regulate branching. The parasite seed then germinates and follows the concentration gradient of the germination stimulant to reach the root. Synthetic strigolactones are available; we use one called GR24 to pre-germinate the seeds before infecting the plant. This is done by prising the lid off the rhizotron and literally "painting" the seeds over the roots. The poor rice plant hasn't got a chance. At this moment, my Striga seeds are still preconditioning in the incubator and my rice plants propped up in their rhizotrons in the controlled growth room chamber, ready for infecting next week. I mustn't forget I'm on water barrel duty this coming week - if everyone's plants die from drought it will be my fault!
 Preparing the Rhizotron - packed with vermiculite with a strip of rockwool at the bottom to stop it falling out.
 In goes the seedling, resting on a strip of mesh
Rhizotrons wrapped in foil and packed into the Controlled Environment Room (CER)...which is a fair bit warmer than outside!

Meanwhile, I am constantly surprised at how much there is going on (perhaps Durham was a bit of a small University in that respect...)... it can be a bit overwhelming at times and I had to be disciplined in NOT attending all the talks at the book festival. I did catch a highly entertaining talk on science communication given by Ed Young, famous for his Blog "Not exactly rocket science" - it certainly gave me a few ideas for shaping this blog. The Animal and Plant Sciences Department, meanwhile, is keenly committed to public outreach, with a highlight this term being the "Christmas Time Lecture" where close on a thousand young school children are treated to a "Royal Society Lecture" experience before hands-on demonstrations and other entertainments. Past topics have included Birds and Dinosaurs and this year Plants have the starring role... I'm keen to be involved but with this literature review hanging over me, I'm not sure I will be able to spare the time to organise a demonstration so perhaps it will have to be as a steward. It will be worth it to see the unveiling of RoboPlant!

Monday 14 October 2013

'A PhD should be regarded as a form of training...'

My supervisor was keen to stress that I was unlikely to make any major, enlightening discovery as we mapped the next four years of my life ( well three, I believe the last year will mainly be spent writing up- if I get any results!). But given that I am investigating an area that is largely unknown ( the metabolic response of host plants when infected with Orobanche or Striga), it will be like leaping into the dark. I will be using a technique called MALDI- MS to measure the profile of metabolites ( the end products of the biochemical reactions that occur in living cells) in the infected host plant. My main task is to compare the profiles of susceptible and resistant host cultivars to see if there are any metabolites associated with resistance ( that could POTENTIALLY be exploited into novel control strategies!). Before I can get any data though, I must first optimise the plants for the MALDI technique ( see paragraph below, 'MALDI in a nutshell') as it hasn't been used for these systems before. And this is where science becomes more like cookery, or craftsmanship; tinkering about with protocols, adjusting conditions, tweaking parameters until the process finally works. I spent a very frustrating summer trying to sequence a gene; the problem was that the reaction ( Poly,erase Chain Reaction DNA amplification) was incredibly sensitive and would only work if the conditions were absolutely right, even a single degree difference in temperature could stop it from working! So I am nervous about how long it will take to get this technique to work. When it DOES though, it will apparently spew out so much data that I will only be able to analyse it using the special computers in the department. So I envisage long, lonely nights, after everyone else has gone home, staring at the screen in a darkened room, trying to make sense of it all....
But first I have to get to that stage!
Meanwhile I have been doing more reading for the literature review. If anything, it has made me aware of how many things I don't know. Such as basic plant families....might be useful for general knowledge crosswords too. And sunflowers....the only thing I knew about these before was that my brother managed to grow the tallest one at school. Today I learnt that there are different kinds for making either oil or confectionary. As always in science, one question leads to another.
I have also been trying to do more other things: I attended my first departmental seminar last week on how plants have been key agents in driving global climate changes in the past by David Beerling ( for more information see his book 'The Emerald Planet'). Unlike many of the seminars I attended as an undergraduate, this one was PACKED and I was lucky to get a space to crouch on the floor! I also went to a 'Women in Science and Engineering' careers event. It was heartening to hear from women who had advanced up the ranks of powerful industrial companies, such as Rolls Royce, and by far the best quote was 'I used to work at Microsoft but it wasn't challenging enough...'

MALDI- MS in a nutshell
In mass spectrometry (MS), samples are vaporised and enter a chamber in which they undergo ionisation to form charged particles ( ions). In "positive ion mode", the sample components are bombarded with a stream of electrons which knocks off negative electrons from the sample atoms, forming positive ions. These are then attracted to a source of negative charge and accelerated, so that they each have the same kinetic energy. They are then deflected by a magnetic field, to an extent which depends on their mass; lighter ions are deflected more than heavier ones. This separates the ions by their mass/ charge ratio, producing a 'profile' of charged particles, allowing the components of the sample to be identified. In MALDI (Matrix Assisted Laser Desorption Ionisation), ionisation is achieved using a UV laser. The sample is first coated in a matrix which absorbs the energy from the laser. This energy is transferred to the sample, releasing ions from the surface which are then separated in the mass spectrometer. 

1. My bench in lab C45

2.The wonderful collection of fridge magnets in the lab


Saturday 5 October 2013

'Everyone flounders during the first week of their PhD...'

...so my supervisor assured me during our first 'official' meeting together when I mentioned that I was feeling a bit lost. Certainly it feels as though I have been thrown into the deep end a bit. I had got used to the intimate, compact nature of Durham - and being able to get to the science site in 3 and a half minutes- so everything here seems on a much larger scale. My room in the Ranmoor postgraduate village is very pleasant: there are eight of us in total on the floor, all with an en suite room and sharing a kitchen/ dining area. My walk into the department though, now takes half an hour, along streets choked with traffic, litter, students and surprisingly expensive 'convenience stores'. Not to mention SubWay outlets...
That aside, the project itself sounds very exciting. My first tasks will involve becoming familiar with growing parasitic plants to take sections from. Apparently, it can be very difficult to infect sunflowers with Orobanche in the lab- usually in agriculture, the problem is that crops are too EASILY infected. However, this lab contains the world experts in Striga and Orobanche and over the years they have developed tried and tested protocols. I will be benefitting from years of hard earned experience!

The growing facilities will be closed down over Christmas for maintenance so I will have to start preparing specimens straight away to have them ready in time. My Maine ask for is term however, is to produce a Literature Review to place my project in the context of work already performed by others ( with so many research labs in the world these days, it is all too easy for different groups to replicate one another's work). Fortunately, I had to prepare a Literature Review as part of my final year at Durham - I chose to compare the similarities between plant interactions with mycorrhizal fungi and nitrogen fixing Rhizobia bacteria- so am familiar with the paper trail that chasing references entrails. Besides the  wonderful, yet occasionally frustrating, referencing software Endnote. It's difficult to know where to start, so I shall just have to dive in and hope that the way ahead will seem clearer as I read...and read... and read....

This week has been a whirlwind of registration tasks and compulsory training sessions, everything from fire safety to waste management. 'At one point we had 27 separate waste streams' the Deaprtmental Technician cheerfully stated 'but that was a bit too much to manage'. There still seem to be an awful lot though, with different boxes and bins depending on whether your waste is hazardous, medically related, infectious...etc. Being so used to science paraphernalia, I find it hard to believe that pipettes tips and latex gloves still require special disposal as these count as 'offensive waste' which could upset members of the public if they came across them. Meanwhile, after the CoSHH ( care of substances hazardous to health) session, I feel that I will be lucky to get any actual research done, with the number of Risk Assessments I will need to do!

More excitingly, I have a desk, a locker and a bench to work at. Now I can feel like a member of the lab, even though I still don't know who everyone is and have forgotten the names of those who I was introduced to. The sooner the promised lab photo board is produced the better! And I have attended my first 'Wednesday morning coffee break', held in the departmental common room at 10.30. Coffee break happens every day, but everyone goes on Wednesday because there are free chocolate biscuits. Apparently, it was the only way to get everyone in one place so that any important announcements could be made...

Hopefully by my next post I will have made some progress with the literature and learning names! Thanks for reading!